# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:07:11 2021
#   Inital geometry file: a 79 line input string
#   Ligand name: 3,4-di-O-sulfo-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O[S](O)(=O)=O)[C@@H]1O[S](O)(=O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 5LT  5LT  3,4-di-O-sulfo-alpha-D-glucopyranose  D-saccharide  32  20  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5LT
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 5LT  C1   C  CH1   0   0.280  102.4751   98.2183  -37.5223
 5LT  C2   C  CH1   0  -0.004  103.4853   99.2359  -37.0068
 5LT  O2   O  OH1   0  -0.651  104.7154   98.5939  -36.8532
 5LT  C3   C  CH1   0  -0.093  102.9981   99.7904  -35.6616
 5LT  O3   O  OC2   0  -0.585  101.8275  100.5951  -35.9121
 5LT  C4   C  CH1   0  -0.020  102.5486   98.7022  -34.6860
 5LT  O4   O  OC2   0  -0.574  103.7645   98.1138  -34.1718
 5LT  C5   C  CH1   0  -0.040  101.7150   97.5999  -35.3420
 5LT  O5   O  O2    0  -0.491  102.2828   97.1964  -36.5652
 5LT  C6   C  CH2   0  -0.171  100.2341   97.9587  -35.4355
 5LT  O6   O  OH1   0  -0.665   99.5586   96.8108  -35.8846
 5LT  S1   S  S     0   1.662  101.8748  102.1668  -35.6900
 5LT  S2   S  S     0   1.657  103.9146   97.9054  -32.6039
 5LT  O13  O  OS    0  -0.705  102.0304  102.2133  -34.1124
 5LT  O11  O  OS    0  -0.622  103.0471  102.7303  -36.3077
 5LT  O12  O  OS    0  -0.604  100.5581  102.6093  -36.0418
 5LT  O23  O  OS    0  -0.701  104.0174   99.3887  -32.0588
 5LT  O21  O  OS    0  -0.609  105.1594   97.2086  -32.4475
 5LT  O22  O  OS    0  -0.628  102.6869   97.3993  -32.0532
 5LT  H1   H  HCH1  0   0.213  101.5263   98.7363  -37.7220
 5LT  H2   H  HCH1  0   0.258  103.5370  100.0697  -37.7201
 5LT  HO2  H  HOH1  0   0.463  105.3920   99.2558  -36.6785
 5LT  H3   H  HCH1  0   0.309  103.7872  100.3889  -35.1954
 5LT  H4   H  HCH1  0   0.304  101.9801   99.1724  -33.8780
 5LT  H5   H  HCH1  0   0.278  101.7709   96.7224  -34.6906
 5LT  H61  H  HCH2  0   0.218   99.9058   98.2633  -34.4332
 5LT  H62  H  HCH2  0   0.215  100.0525   98.8103  -36.0982
 5LT  O1   O  OH1   0  -0.654  102.9721   97.6383  -38.6666
 5LT  HO1  H  HOH1  0   0.466  102.2459   97.2411  -39.1589
 5LT  HO6  H  HOH1  0   0.460   98.6294   97.0349  -35.9871
 5LT  H13  H  H     0   0.520  102.7668  102.7811  -33.8276
 5LT  H23  H  H     0   0.515  104.8901   99.7889  -32.2168

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 5LT  C1   O5   single  1.413  0.020  1.413
 5LT  C1   C2   single  1.524  0.020  1.524
 5LT  C2   C3   single  1.534  0.020  1.534
 5LT  C2   O2   single  1.396  0.020  1.396
 5LT  C3   O3   single  1.442  0.020  1.442
 5LT  C3   C4   single  1.529  0.020  1.529
 5LT  O3   S1   single  1.588  0.020  1.588
 5LT  C4   C5   single  1.530  0.020  1.530
 5LT  C4   O4   single  1.445  0.020  1.445
 5LT  O4   S2   single  1.589  0.020  1.589
 5LT  C5   O5   single  1.408  0.020  1.408
 5LT  C5   C6   single  1.527  0.020  1.527
 5LT  C6   O6   single  1.406  0.020  1.406
 5LT  S1   O12  double  1.433  0.020  1.433
 5LT  S1   O11  double  1.440  0.020  1.440
 5LT  S1   O13  single  1.586  0.020  1.586
 5LT  S2   O22  double  1.438  0.020  1.438
 5LT  S2   O21  double  1.435  0.020  1.435
 5LT  S2   O23  single  1.584  0.020  1.584
 5LT  C1   H1   single  0.970  0.020  1.090
 5LT  C2   H2   single  0.970  0.020  1.090
 5LT  O2   HO2  single  0.850  0.020  0.980
 5LT  C3   H3   single  0.970  0.020  1.090
 5LT  C4   H4   single  0.970  0.020  1.090
 5LT  C5   H5   single  0.970  0.020  1.090
 5LT  C6   H61  single  0.970  0.020  1.090
 5LT  C6   H62  single  0.970  0.020  1.090
 5LT  C1   O1   single  1.376  0.020  1.376
 5LT  O1   HO1  single  0.850  0.020  0.980
 5LT  O6   HO6  single  0.850  0.020  0.980
 5LT  O13  H13  single  0.850  0.020  0.980
 5LT  O23  H23  single  0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 5LT  O1   C1   H1   111.06  3.000
 5LT  O1   C1   O5   107.91  3.000
 5LT  H1   C1   O5   110.26  3.000
 5LT  O1   C1   C2   108.87  3.000
 5LT  H1   C1   C2   108.60  3.000
 5LT  O5   C1   C2   110.12  3.000
 5LT  H2   C2   C3   108.05  3.000
 5LT  H2   C2   O2   112.28  3.000
 5LT  C3   C2   O2   110.46  3.000
 5LT  H2   C2   C1   108.57  3.000
 5LT  O2   C2   C1   108.32  3.000
 5LT  C3   C2   C1   109.11  3.000
 5LT  HO2  O2   C2   108.85  3.000
 5LT  H3   C3   C4   109.22  3.000
 5LT  H3   C3   O3   110.73  3.000
 5LT  C4   C3   O3   105.62  3.000
 5LT  H3   C3   C2   110.00  3.000
 5LT  C4   C3   C2   113.30  3.000
 5LT  O3   C3   C2   107.88  3.000
 5LT  S1   O3   C3   120.25  3.000
 5LT  H4   C4   C5   110.07  3.000
 5LT  H4   C4   O4   110.45  3.000
 5LT  C5   C4   O4   108.52  3.000
 5LT  H4   C4   C3   108.55  3.000
 5LT  O4   C4   C3   105.63  3.000
 5LT  C5   C4   C3   113.53  3.000
 5LT  S2   O4   C4   118.94  3.000
 5LT  H5   C5   C6   105.93  3.000
 5LT  H5   C5   O5   105.47  3.000
 5LT  C6   C5   O5   113.92  3.000
 5LT  H5   C5   C4   107.14  3.000
 5LT  C6   C5   C4   112.68  3.000
 5LT  O5   C5   C4   111.06  3.000
 5LT  C5   O5   C1   115.85  3.000
 5LT  H62  C6   H61  106.70  3.000
 5LT  H62  C6   O6   111.24  3.000
 5LT  H61  C6   O6   112.00  3.000
 5LT  H62  C6   C5   112.40  3.000
 5LT  H61  C6   C5   107.42  3.000
 5LT  O6   C6   C5   107.09  3.000
 5LT  HO6  O6   C6   107.95  3.000
 5LT  O12  S1   O11  121.46  3.000
 5LT  O11  S1   O13  109.60  3.000
 5LT  O12  S1   O13  108.98  3.000
 5LT  O13  S1   O3    99.85  3.000
 5LT  O11  S1   O3   110.58  3.000
 5LT  O12  S1   O3   104.12  3.000
 5LT  O22  S2   O21  121.88  3.000
 5LT  O21  S2   O23  111.16  3.000
 5LT  O22  S2   O23  104.67  3.000
 5LT  O23  S2   O4   102.88  3.000
 5LT  O21  S2   O4   104.67  3.000
 5LT  O22  S2   O4   110.10  3.000
 5LT  H13  O13  S1   112.50  3.000
 5LT  H23  O23  S2   112.80  3.000
 5LT  HO1  O1   C1   109.07  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 5LT  Var_01  O12  S1  O3  C3  179.65  30.0  3
 5LT  Var_02  O22  S2  O4  C4   42.58  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 5LT  chir_01  C1  O5  C2  O1  negativ
 5LT  chir_02  C2  O2  C1  C3  negativ
 5LT  chir_03  C3  O3  C4  C2  negativ
 5LT  chir_04  C4  O4  C3  C5  negativ
 5LT  chir_05  C5  O5  C4  C6  negativ

